The Dice and Tanimoto similarity functions available in RDKit are able to handle fingerprints corresponding to both IntVect and BitVect. All other similarity functions, however, expect BitVect fingerprints to calculate pairwise similarity. Consequently, ExplicitBitVect fingerprints are generated for AtomPairs, Morgan, MorganFeatures, and TopologicalTorsions for similarity calculations instead of default IntVect fingerprints.

A comma delimited list of parameter name and value pairs for writing molecules to files. The supported parameter names for different file formats, along with their default values, are shown below:

Default value for compute2DCoords: yes for SMILES input file; no for all other file types.

--overwrite

Overwrite existing files.

-p, --paramsFingerprints <Name,Value,...> [default: auto]

Parameter values to use for generating fingerprints. The default values are dependent on the value of '-f, --fingerprints' option. In general, it is a comma delimited list of parameter name and value pairs for the name of the fingerprints specified using '-f, --fingerprints' option. The supported parameter names along with their default values for valid fingerprints names are shown below:

AUTHOR

SEE ALSO

COPYRIGHT

The functionality available in this script is implemented using RDKit, an open source toolkit for cheminformatics developed by Greg Landrum.

This file is part of MayaChemTools.

MayaChemTools is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.